For nearly five years, the Public Corruption and Civil Rights section of the U.S. attorney’s office had been building and winning cases against a group from the Los Angeles County Sheriff’s Department accused of carrying out a plan to obstruct a federal investigation into allegations of inmate abuse at the county jails.

The prosecutors worked their way up the chain of command. But when it went after its last and largest target — former Sheriff Lee Baca — the government’s run of wins came to an abrupt end this week.

The mistrial declared Thursday after jurors deadlocked 11 to 1 in favor of acquitting Baca of conspiracy and obstruction of justice charges affirmed what even prosecutors knew going into the trial: Convicting Baca would be much harder than the others.

In the end, the government failed to convince all but one juror that Baca had harbored malicious intent and played a direct role in the plot to interfere with federal authorities, an outcome that underscores the difficulty of trying to tie top public officials to corruption carried out by subordinates, interviews with jurors and legal experts showed.

“It is always challenging to pursue cases such as these, where the government is seeking to hold criminally responsible a highly regarded public servant at the highest levels of law enforcement,” said Miriam Krinsky, a former federal prosecutor who led a commission on jail violence and who has closely followed the trial. “The prosecution of an iconic and respected figure such as Lee Baca was particularly challenging.”

The government itself acknowledged the weaknesses underlying its case in court papers related to a deal that Baca and prosecutors struck earlier this year.

In June, Assistant U.S. Atty. Brandon Fox, the lead prosecutor in the obstruction cases, filed a memo explaining why the judge should approve the deal. Under the terms of the agreement, Baca would plead guilty to a lesser charge of making a false statement to federal investigators in exchange for no more than six months in prison.

The proposed time behind bars was significantly less than the sentences U.S. District Judge Percy Anderson had given to the defendants in the other obstruction cases, and Fox tried to convince Anderson that the comparatively light punishment was justified because the evidence against Baca was relatively weak.

“While he was at the top of the organization, the evidence does not show that he was as involved…as his subordinates were,” Fox wrote. Fox declined to be interviewed for this article.

In his memo, the veteran prosecutor went through the various aspects of the obstruction scheme, which included hiding from FBI agents an inmate who was working as their informant, witness tampering, and intimidating the lead agent in the case.

For each, Fox wrote, “The investigation has revealed no evidence that defendant Baca was aware.” By contrast, prosecutors had managed to win a conviction against Baca’s top aide, then-Undersheriff Paul Tanaka, on a bounty of emails, phone records and other evidence that showed he had led the group that carried out the alleged scheme.